Fun with patents

One of my automated PubMed searches just brought up a paper that’s well outside the scope of my usual reading material. I’m glad I persevered with it, though, because this is a very important paper that highlights the dangers inherent in patents on gene sequences.
Thomas Kepler, Colin Crossman, and Robert Cook-Deegan from Duke University in North Carolina assessed the reach of a patent on the sequence of the human BRCA1 gene, a major susceptibility locus for breast and ovarian cancer. Women with a family history of these cancers are routinely referred for BRCA1 and BRCA2 mutation testing, and positive results have serious enough ramifications for the patient and her relatives that DIY testing would be an incredibly bad idea.
A company called Myriad Genetics currently holds patents relating to BRCA1 and BRCA2 testing, patents that technically prohibit any other entity from carrying out these important genetic tests (the Canadian Cancer Society have a synopsis of the current state of affairs on their website).
The paper by Kepler et al., cleverly titled “Metastasizing patent claims on BRCA11, analyses the impact of one particular part of the patent claim, a claim that seemed “particularly broad”:

“The patent first makes claim 1, to “An isolated DNA coding for a BRCA1 polypeptide, said polypeptide having the amino acid sequence set forth in SEQ ID NO:2.” SEQ ID NO:2 is the 1863-residue amino acid sequence for the protein encoded by the BRCA1 gene. The patent further claims “5. An isolated DNA having at least 15 nucleotides of the DNA of claim 1.” Note that claim 1 is DNA coding for the polypeptide, not for any specific gene. There are, of course, many polynucleotides that would encode the BRCA1 polypeptide. Claim 5, then, is a claim on any 15-mer oligonucleotide found in any such sequence.”

The authors used some fancy-pants numbersmithin’ to assess the reach of this patent claim, and estimate that:

“the human genome contains over one million oligonucleotides covered by this claim, and that most human genes contain at least one and usually several oligonucleotides covered by the claim.”

The estimate appears to stand up after some fancy-pants samplin’ and other analyses.
Having sequenced my fair share of DNA as part of completely non-BRCA1-related projects, I’m probably in breach of this patent myself, and I’d be willing to bet that a fair percentage of the people reading this blog post are too. And interestingly, this very fact may represent grounds for ruling the patent invalid; the vast majority of gene sequences submitted to GenBank before the patent was filed contain the offending oligonucleotides. There goes that novelty claim, then…
This paper is a very creative (and hopefully effective) way to highlight the perils of patents on gene sequences, a practice that I personally have never understood and think should be decisively (and retroactively) banned. The BRCA patents are currently the subject of a lawsuit brought against Myriad Genetics by the American Civil Liberties Union and other entities, including scientific associations and patient advocacy groups. It goes without saying that the results of the lawsuit are of paramount importance, and very eagerly awaited…
1. The paper is currently an uncorrected proof in the journal Genomics. doi:10.1016/j.ygeno.2010.03.003

About Cath@VWXYNot?

"one of the sillier science bloggers [...] I thought I should give a warning to the more staid members of the community." - Bob O'Hara, December 2010
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20 Responses to Fun with patents

  1. Kausik Datta says:

    You do automated PubMed searches? For fun?

    Faints *

  2. Cath Ennis says:

    Well, yes, on other topics. But this one actually came up in one of my work-related searches 🙂

  3. Austin Elliott says:

    You should try contacting Prof John Sulston and asking him about this, Cath. He is very interested in what I might call “ethical aspects of IP”, and I’m pretty sure I remember him writing a bit about the Myriad / BRAC1/2 story in his autobio The Common Thread.
    Perhaps I’ll email him a link to this blog.

  4. Cath Ennis says:

    EEK! But he’s, like, really really famous! I wouldn’t dare!

  5. Cath Ennis says:

    Especially because I wrote things like “fancy-pants numbersmithin'”. GAAH!

  6. Frank Dondelinger says:

    Very interesting! I wrote an article about gene patenting a while back (available here: (page 16) in case you’re interested).
    I always suspected that gene patenting was a silly idea, but this patent takes silly to a whole new level…

  7. Cath Ennis says:

    Very nice article, Frank – thanks for the link! I like the idea of open source science. I’m all for individuals and corporations being able to recoup their investments by protecting their IP, but clearly the current paradigm is inhibiting progress.
    Silly is a very apt word. (In fact, after I published this post, I realised that “patently absurd” would have been a much better title. But I’m still learning the new blogging software that we just switched to, and I’m too scared to change the title!) How you can claim to have invented something that is clearly a discovery is beyond me, but then I’ve never had the benefit of a law school education 🙂

  8. Richard Wintle says:

    Cath – I used John Sulston’s old stereo microscope for ten days during a practical course, and actually met the gentleman. Famous, yes. Scary, not so much. 😉
    The Province of Ontario’s healthcare system had a memorable scrap with Myriad over BRCA1/2 testing as I recall.
    Fun fact: a good chunk of the research resulting in the identification of BRCA1/2 was done right here at SickKids. The person involved was in my office about an hour ago. 🙂

  9. Austin Elliott says:

    That (where the work that ended up generating the BRCA1/2 sequence was done) is one of the things Sulston discusses in The Common Thread. The book (co-written with Georgina Ferry) is a really good read, esp. if you want to find out what Sulston thinks about stuff related to the Human Genome Project, e.g. Craig Venter and the “patenting genes for profit” movement.

  10. Cath Ennis says:

    Richard, I had a rather traumatic experience with a very very famous scientist in the first year of my PhD. I may well be scarred (and scared) for life 🙂
    BC is still doing its own BRCA testing AFAIK. I know a lot of people who will be following the current lawsuit very closely…
    Austin, I’ll put it on my list!

  11. Åsa Karlström says:

    cath: I love that story. I’m sure it was all perfectly fun for everybody involved 😀
    I had somehing more on topic to say about the patent but I’ll have to wait for tomorrow morning. My brain is shutting down at the moment and I can’t form a good sentence.

  12. Richard Wintle says:

    Austin – thanks for the tip. I’d read that Dr. Sulston is an advocate for open-ness and non-commercial approaches (oddly enough, I read this in a book by James Watson). There are good parallels to be drawn between he and Maurice Wilkins, who also took a very humanist approach to science (autobiography highly recommended, at least by me).
    In fairness, I believe Dr. Venter was pushed by NIH to file many of those gene patents. His autobiography is next on my reading list, naturally.

  13. Social comments and analytics for this post

    This post was mentioned on Twitter by NatNetNews: Problems with patents – @enniscath highlights a recent paper on BRCA1 testing: #NatNet

  14. Sonja Babovic says:

    The US Secretary’s Advisory Committee on Genetics, Health, and Society just recently issued a report proposing a few legal changes to the current system:
    1) An exemption from liability for anyone who infringes a patent on a gene while making, using, ordering, offering for sale, or selling a genetic test for patient care purposes.
    2) The creation of an exemption from patent infringement liability for those who use patent-protected genes in the pursuit of research.
    It will be interesting to see where this goes. You can read the report (all 107 pages of it) at
    I met Sir Sulston last summer (and he is indeed not scary at all)… looking back, I’m surprised that I was at all shy about asking CC if I could leave work early to have lunch with a Nobel laureate!

  15. Austin Elliott says:

    Some people have a mode radical view of the current system of Pharma R&D / patenting / pricing. See a recent Comment piece in the Guardian.
    And a view of patenting and IP from John Sulston and friends, also in the Guardian, is here.

  16. Austin Elliott says:

    I emailed a link to this post to John Sulston: here is part of his reply:

    “Great paper from Duke, and congrats to Cath Ennis on her blog…

    I’m slightly involved (merely as a named supporter) with the ACLU case against Myriad. Will be interesting to see where it goes…

    We have an event at the Royal Society in May, debating the Manchester Manifesto (PDF) with the association of IP attorneys. Should give [the issues] a bit more of an airing.”

    [Small edits mine, and link added]

  17. Cath Ennis says:

    Chall, well I can only speak for myself when I say “not really” 🙂
    Richard, I bet Venter’s autobiography is a good read! Please let us know when you’ve finished it!
    Sonja, thanks for the link! I probably won’t read the entire document to be honest, but I’ll have a quick browse of it later! The suggestions you quoted are very encouraging; perhaps some common sense is returning to this field.
    Austin, very interesting articles – thanks for pointing them out! And thanks also for passing this link on to John Sulston (eek…) Thanks also to you and Frank for tweeting a link to this article to Ben Goldacre, who retweeted it to his followers. Serious geek cred points for me that day… if only I could see my stats (hint hint 🙂 )

  18. Austin Elliott says:

    Via Times science editor Mark Henderson’s Twitter feed, an analysis of the Myriad decision from two patent lawyers, one of them a law Prof specialising in IP:

  19. Cath Ennis says:

    Ah, good stuff – I don’t need to write anything myself now 🙂
    The article confirmed my assumption that there will probably be an appeal. It’ll be very interesting to see where this goes. If this ruling stands, I wonder if there will be any repercussions for the people who granted the patents in the first place?

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